Problem 14
The Energetic Cost of Mismatch Repair In an \(E\). coli cell, DNA polymerase III makes a rare error and inserts a G opposite an A residue at a position \(650 \mathrm{bp}\) away from the nearest GATC sequence. The mismatch repair system accurately repairs the mismatch. How many phosphodiester bonds derived from deoxynucleotides (dNTPs) does this repair expend? This process also uses ATP molecules. Which enzyme(s) consume the ATP?
Problem 16
DNA Repair and Cancer Many pharmaceuticals used for tumor chemotherapy are DNA damaging agents. What is the rationale behind actively damaging DNA to address tumors? Why do such treatments often have a greater effect on a tumor than on healthy tissue?
Problem 17
Direct Repair Cells normally repair the lesion \(O^{6}\)-meG by directly transferring the methyl group to the protein \(O^{6}\) methylguanine-DNA methyltransferase. For the nucleotide sequence \(\mathrm{AAC}\left(O^{6}-\mathrm{meG}\right) \mathrm{TGCAC}\), with a damaged (methylated) G residue, what would be the sequence of both strands of double- stranded DNA resulting from replication in each of the situations listed? a. Replication occurs before repair. b. Replication occurs after repair. c. Two rounds of replication occur, followed by repair.
Problem 18
Strand Invasion in Recombination A key step in many homologous recombination reactions is strand invasion (see step 2 in Fig. 25-29). In almost every case, strand invasion proceeds with a single strand that has a free \(3^{\prime}\) end rather than a \(5^{\prime}\) end. What DNA metabolic advantage is inherent with the use of a free 3 ' end for strand invasion?
